Jax, Me, and the Surf

Jax, Me, and the Surf

Reefkeeping Made Easy - What Was Not Explained (Fact Sheet)

Reefkeeping Made Easy
What Was Not Explained

Hosted by Geoff
Contributions by: Fat Tony, wharyat, dmora723, chrisd, Elegance Coral, embross67, Nate_Bro, FutureDoc, et al.

The biggest things we will be discussing in this document are the biological process that are going on in our systems. These biological process are what most of the false information that is out there is about. This includes reef forums and LFS.

The two main elemental processes we will be discussing are the Nitrogen and Phosphate cycles that are occurring in our systems. these two elements lead to the greatest confusion about what is going on in our little slices of ocean.

I am tired of all of the bad info that is out there. We need to get this hobby under control or it will not make it much longer with all of the environmental trouble that is going on around the world. This hobby of ours is actually pretty self sustaining if we just understand the basics.
Nitrogen Cycle


The process of ammonia to nitrite and nitrite to nitrate takes place in oxygenated areas.

Nitrates are a great algae fertilizer.

The greater the flow, the longer detritus remains suspended to be removed by filtration. This assists in removing the products that fuel the nitrogen cycle to begin with.


The process of nitrates to N gas takes place in anoxic areas. The best place for this is live rock.

Sand beds can also process nitrate to N gas, but live rock is more efficient – substrate is a 2 dimensional surface.

All of the bacteria that handle the entire process reside very close to each other. With one layer feeding the other. This is why when the nitrates are free they can not get to the anoxic layers because they are already feeding on the nitrates that the layer right next to them are supplying them.

An excess of nitrates means there is an imbalance between the amount of aerobic areas and anoxic areas.
Phosphates are needed for all life.

They come in two forms – orthophosphates and inorganic phosphates.

All food contains both types of phosphates.

Phosphates are mined from limestone, or any large deposits of calcium carbonate. Calcium carbonate is a great phosphate binder. Live rock, aragonite sand, and coral skeletons are all composed of calcium carbonate, which means they also contain phosphates.

Imported organic phosphates break down very quickly in the SW environment to orthophosphates which are then immediately taken up by the organisms in the system.

High phosphate levels restrict the calcification of salt water which prevents healthy growth of corals, inverts and coralline algae. But phosphates also contribute to alkalinity levels helping to buffer them higher which in turn helps to buffer pH causing less stress for fish and other inhabitants.

It's important to understand that systems cannot be rid of phosphate. There is phosphate available in every healthy reef tank. Even those low nutrient demanding SPS corals can not grow or replace tissue without phosphate. The goal isn't to eradicate phosphate. It's simply to keep the concentrations below levels that can fuel rapid growing organisms like hair algae.


Orthophosphates make a great fertilizer for algae.

It is hard to get any reading when testing for orthophosphates in a working system. The the cyano/algae/bacteria all want this and will uptake it immediately, binding all orthophosphates and providing your phosphate test kit with a “0”.

When you are actually getting a reading it means that all of the bacteria in your system has bound all of the orthophosphates it can and now there is some free in the water column. 

Orthophosphates are system limiting - if you have very little, you will have very little available for algae/cyano growth.

Algae grows as close to the supply of food as possible.
Phosphates, Live Rock and Substrate

Purging Phosphates from Live Rock

Bacteria in the LR are able to break off bound phosphates that are attached to the calcium carbonate. They then incorporate it into their bodies and bind it. The more phosphates the more bacterial bodies. When you get enough bacteria together they create a fair amount of force. This force pushes the dead bacterium (bacterial flock) out of the LR where it can then be swept away from the LR. This bacterial flock is heavier then water so it falls to the bottom, or if your water flow is strong enough it can get pushed around until 1) it gets removed by the skimmer or 2) settles somewhere. either in a hard to reach low flow area or your sump/fuge. if this is planned then it is all good. If you have more sand in these areas then not so good. The force that the bacteria exert is known as Turgor. this makes LR self cleaning when it comes to phosphates.

Live rock will wick phosphates up from the substrate if in direct contact with it. To prevent this, use supports to suspend live rock above the surface of the substrate.

Buildup of Phosphates in Substrate

Bacterial Turgor also happens in the substrate. But the problem with sand is that it is contained on every side but the top. so the bacterial flock formed from the LR and the sand just keeps building up in the sand bed till it just gets full. At the point the Turgor is pushing the flock up into the water column is when you are able to get phosphate readings from the test kits.

Phosphates can be kept in control by siphoning the substrate thoroughly. There is nothing living in your sand bed that is not already living in your LR. Populations from the LR will quickly repopulate any empty places in your sand bed.

The greater the flow, the longer detritus remains suspended to be removed by filtration.
Live Rock

Anoxic (denitrifying) layers can be considered “safer” in Live Rock vs. substrate. These areas in rock can be easily purged as long as nitrates and phosphates are kept to levels that will not overload the rock.

Porous live rock is better from a filtration point of view. The less dense, the more nooks and crannies in it for bacterial colonization.

Purchasing dry rock in lieu of fresh live rock is the safest. Allow nitrosomona and nitrobacter bacteria grow, and the risk of introducing bad hitch hikers is removed. Then get the coraline from a fellow reefer, if you want to add that to your system.

Cured live rock does not contain much of the unwanted critters nor much in phosphates.

If you do not have access to cured rock, you can cook live rock by placing it in containers of artificial saltwater with a power head for flow. As the rock purges itself, bacterial flock will be evident at the bottom of the container. Swish the rock (to remove any loose bacterial flock), siphon and replace the water on a weekly basis as the rock sheds. The rock will be cured when very little flock is visible at the bottom of the container prior to the regularly scheduled water change.

Cooking rock does not require light or heat unless a hitchhiker is to be kept. Nitrifying bacteria will continue to grow in temperatures ranging from 64 – 100 degrees plus. However they thrive in the range of 77 – 86 degrees. But keeping the water at reef temperature (78-80 degrees) will speed up the metabolism of the bacteria, allowing them to process phosphates in the rock faster.

Fresh live rock with the most growth on it is generally harvested in areas that tend to be lagoons. Algae likes high nutrient water, and nutrients settle out in low flow areas, such as lagoons. Live rock from these areas are already loaded with phosphates.

Concerning denitrification, there is nothing wrong with coralline covered rock. It tends to not block the LR as much as you would think. Also if coralline is able to cover your LR then it is not full of phosphates. If it were then the phosphates would actually hinder the growth of coralline algae completely. The phosphate can hurt in the production of calcium carbonate into the skeleton when present in large quantities.

In “low-poo” systems, less than 1 lb per gallon is required for adequate live rock filtration.
Live Sand

Don't ever buy live sand. How can it be live if it is in a bag of water? At that point it's just more phosphates to add to your system.

Jump start your system with a very small piece of LR from a system you trust. The smaller the better. That allows it to be scrutinized and ensures there are no unwanted hitchhikers on it. Even a tiny piece of live rock will contain the bristleworms and pods that everyone needs in their system.
Early Tank Processes

Not only do new tanks start with the nitrogen cycle, but also the silica and phosphate processes. The latter two processes start at around 2-3 weeks and can continue for months. They are commonly referred to as “the uglies”.

Silica and phosphates are made almost immediately available to the system due to the mechanical means of setting up an aquarium. As bits of sand and LR rub against each other they break off little bits. These little bits allow the silica and phosphates to become loose in the water column. The more sand/LR the greater the chance of having more of these available right after the system is setup.

Silica Processes

The main algae that needs scrapped off the glass is diatomic. It uses silica in its body structure. In the beginning of a system, diatomic algae is the only real user of silica. It quickly is able to ramp up and bloom to use up significant amounts of the silica, hence the brown algae bloom encountered.

Over time as the tank matures, sponges will start growing under the LR. These sponges also need the silica and will quickly start uptaking the silica making it less available to the diatomic algae.

Soft corals and perhaps LPS also use silicates in their structure.

Sponges and some coral bind up the silicates long term – unlike the diatomic algae which reproduce and die fairly rapidly releasing and uptaking the silicates. Until these binding organisms take off the diatomic algae bloom will continue.

Phosphate Processes

Cyanobacteria and algae are the first organisms to process phosphates.

Phosphates do not cycle per se. Rather they fluctuate. They are bound by living organisms and are released as those organisms die.

Bacteria is the fastest at being able to uptake phosphates. Algae is second. In an empty system it is a race between bacteria and algae to deplete the phosphate in the water column.

As the phosphates are used up they are deposited on the substrate in a nice layer. This is where the cyano come in. They grow where the nutrients are, This is helpful to us because it gives us something to siphon.

Removing the cyano will remove the phosphates in its biomass. What we are waiting to happen to finally bring the "uglies" to an end is for the phosphate laden material to either be removed or sunk somewhere that is unavailable to the algae and bacteria.
Macro Algae

If macro algae is growing then there is a phosphate problem. The macro algae is just another phosphate sponge. If it is able to find phosphates then the calcium carbonate structures are full and are now leaching the phosphates back into the system fueling the algae. Siphoning the sand bed with every water change will keep the phosphate level under control in the sand bed.

Algae do bind phosphates, but they are also leaky. And like any other organism they have biological functions. They have wastes they need to get rid of also.

Deep Sand Beds (DSBs)

DSB's should be thought of as a nutrient sink or filter. All filters must be cleaned or eventually replaced.

The layers of bacterial activity will start to creep higher and higher as the DSB fills with phosphates. When the DSB is new the bacteria are working everywhere, but as the bed fills up with detritus the bacteria have to move higher in order to not get choked out by the detritus. When a bed is deep cleaned it opens the bed up again and allows the bacteria to function throughout the entire vertical range of the substrate again.

Substrate Husbandry

Siphon the substrate thoroughly with each water change. There is nothing living in your sand bed that is not already living in your LR. Populations from the LR will quickly repopulate any empty places in your sand bed.

When doing water changes, the biggest sources of waste need to be gone after, That is the detritus you see on top of the substrate. The point of water changes is to remove wastes. There are very little wastes in the water column itself, so just changing the water does little, but replace trace elements, which of course are called trace for a reason.

Dead bacteria that contain bound phosphates in their cell structures are expelled from the LR where the flow is able to sweep it away from the LR and allows it to settle elsewhere. In nature it is either in the abyss or in lagoonal areas. We all know what eventually happens to the phosphates in the abyss (think plate tectonics). That is how the reef cleans itself. The phosphates just get dumped someplace else, far enough away so that it is not in the same water column. A substrate siphon IS our abyss.

When doing water changes the biggest source of phosphates could be the replacement water itself. This is why it is recommended that all water going into the tank be RO/DI water. We add a lot of water to our systems through water changes and top off. Keeping this source as phosphate free is possible goes a long way to keeping it under control in the system.

Live Rock Husbandry

Live Rock is self-cleaning provided enough flow is given to wash detritus from it's surface.

Suspend Live rock above the substrate to avoid phosphates from wicking up from the sand into the live rock.

With the amount of flow needed to keep live rock clean, it is suggested to go with CC sand instead of the oolitic sand that is the norm. It is hard to siphon oolitic substrate without siphoning it up.

Bacterial Flock and Detritus

Strategic flow should be used to get the detritus suspended, then forced in the correct direction for removal. Either towards the overflow or intake of the skimmer (HOB).

Suspended detritus needs do be removed so it degrades as little as possible. The only way to completely remove it from contact with the system water is through the use of a skimmer.

Water changes and aggressive siphoning of the substrate will also remove detritus.

Skimmers are the only piece of equipment we reefers have at our disposal that actually removes nutrients from the water column immediately. Every other filter we use traps the detritus and can allow it to rot till we actually remove it manually. This includes reactors, filters, and sand.

A trick to make your skimmer even more efficient is to plumb a UV clarifier immediately before the skimmer. This way anything that the UV killed or broke down would be taken out by the skimmer and not allowed to rot elsewhere in the system.
Reef Lighting and Coral Coloring

All organisms need down time to actually grow and prosper. Therefore it is not recommended to leave the lights on 24/7.

The zoax (browns and greens) in the corals are responsible for the photosynthesis and food production along with the formation of the coral skeleton as a by product of the photosynthesis.

The other colors we see are from proteins the coral produces to block light getting to the zoax to keep the zoax from producing to much oxygen and poisoning the corals.

An overproduction of zoax (browns and greens) in corals are caused by excess nutrients in the water. Zoax (photosynthetic algae) feed on phosphates and nitrates.

Higher temperatures cause higher metabolic rates. Zoax can cause O2 poisoning in coral. The coral will then reduce zoax levels by expulsion. The result is a bleached coral.

Too much light can also cause zoax to O2 poison it's host coral, causing bleaching.

Most of the fish we like to keep fall into the planktonivore category. They feed over the entire day whenever food becomes available. The greatest number of reef safe fish will fall into this category. There are also several species of some non-reef safe fish that can be kept in a reef just fine because they are planktonivores. Genicanthus angels, Hemitaurichthys butterflyfish, and Xanthichthys triggerfish are examples. Several of these fish have been difficult to keep because of the fact that we have been told to keep feeding down in order to keep the nutrients down, which is very important. But what happens if you do not have to worry about keeping nutrients down because you are easily able to remove all detritus? When a BB system is run, one can easily see the detrital build up and are able to control the amount of phosphates in the system. This works with whatever biotope you are trying to do, whether it is a lagoon or a reef top. Being able to keep track of the detritus puts you in charge and not the sand. You are no longer reacting to the bacterial flux going on in the sand bed. With good flow all around the LR then it will remain relatively constant in its phosphate purging.

it is important when feeding to make sure the food is low in orthophosphates. Find a brand that does not have any preservatives listed on their food labels.

Blender mush is another very good type of food - lightly blended so as to produce the greatest difference in sizes of bits. You want everything from coral eating size to fish eating size. Everybody has their own size food they would prefer. This is especially true of corals and some echinoderms.

All SW critter purchases should be researched before hand. Some have a very specific diet that may not be able to be provided for.

During the initial setup period of a tank with all the free organics, you could also see population blooms of other organisms that feed off the organisms that feed off the free phosphates. The most common of these being pods. There will be a large population of pods that will spike about the 6 month mark when a system is just setup. This population will ultimately crash by the 1 year mark and will settle out. It is very tempting to think you can support a pod eating fish when you see all of these pods, but that is a very short term bloom. This is why it is recommended to wait at least a year before determining if the pod population is large enough to support a predator.



Carbon dosing (vodka, vinegar, white sugar) is utilized to reduce nitrates and phosphates and generally adds clarity to the water. However a skimmer is a necessity with this method.

Carbon dosing works by causing an increase in bacteria. That bacteria fill the water column up-taking nitrates and phosphates. The skimmer then removes the bacteria, along with their bound nitrate and phosphate and exports it from the system.

Carbon dosing will allow increased feeding schedule due to the lower nutrients. Note that good husbandry will also allow the same without the dosing.

Carbon dosing also allows the environment to be pushed more toward an ultra-low nutrient system more suitable for SPS coral.

By introducing more carbon in the water column, it allows bacterial to out-compete algae for nitrates and phosphates. Be warned – an increase in bacterial load can deplete oxygen in the system causing the higher organisms stress or death.

Increased coloration in corals have been reported due to feeding on the increase in bacteria in the water column. Corals have also been reported to pale over time.

Kalkwasser (Lime water)

Kalk, lime water, or pickling lime can be used as an economical means of calcium supplementation and results in the raising of pH levels.

It can also reduce levels of magnesium and phosphate indirectly.

It is normally dosed through top-off water.

1 comment:

  1. Dmora723 here. I'm so glad to see this. Great job.
    Special thanks to Geoff.